[lt@localhost pancreas_]$ trim_galore -q 20 --rrbs --fastqc pancreas
Multicore support not enabled. Proceeding with single-core trimming.
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.0
single-core operation.
No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)
AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> pancreas <<)
Found perfect matches for the following adapter sequences:
Adapter type Count Sequence Sequences analysed Percentage
Illumina 45 AGATCGGAAGAGC 1000000 0.00
smallRNA 0 TGGAATTCTCGG 1000000 0.00
Nextera 0 CTGTCTCTTATA 1000000 0.00
Using Illumina adapter for trimming (count: 45). Second best hit was smallRNA (count: 0)
Writing report to 'pancreas_trimming_report.txt'
SUMMARISING RUN PARAMETERS
==========================
Input filename: pancreas
Trimming mode: single-end
Trim Galore version: 0.6.6
Cutadapt version: 3.0
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length before a sequence gets removed: 20 bp
File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction
Running FastQC on the data once trimming has completed
Cutadapt seems to be fairly up-to-date (version 3.0). Setting -j 1
>>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<<
This is cutadapt 3.0 with Python 3.7.2
Command line parameters: -j 1 -e 0.1 -q 20 -a X pancreas
Processing reads on 1 core in single-end mode ...
[-------->8 ] 00:01:14 9,940,000 reads @ 7.5 µs/read; 8.00 M reads/minute10000000 sequences processed
[ 8=------] 00:02:29 19,880,000 reads @ 7.5 µs/read; 8.04 M reads/minute20000000 sequences processed
[---=8 ] 00:03:44 29,960,000 reads @ 7.5 µs/read; 7.96 M reads/minute30000000 sequences processed
[----=8 ] 00:04:28 35,737,506 reads @ 7.5 µs/read; 8.00 M reads/minute
Finished in 268.12 s (8 µs/read; 8.00 M reads/minute).
=== Summary ===
Total reads processed: 35,737,506
Reads with adapters: 0 (0.0%)
Reads written (passing filters): 35,737,506 (100.0%)
Total basepairs processed: 1,286,550,216 bp
Quality-trimmed: 0 bp (0.0%)
Total written (filtered): 1,286,550,216 bp (100.0%)
=== Adapter 1 ===
Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times
>>> Quality trimming completed <<<
35737506 sequences processed in total
Writing final adapter and quality trimmed output to pancreas_trimmed.fq
>>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file pancreas_qual_trimmed.fastq <<<
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
This is cutadapt 3.0 with Python 3.7.2
Command line parameters: -j 1 -e 0.1 -O 1 -a AGATCGGAAGAGC pancreas_qual_trimmed.fastq
Processing reads on 1 core in single-end mode ...
Finished in 286.71 s (8 µs/read; 7.48 M reads/minute).
=== Summary ===
Total reads processed: 35,737,506
Reads with adapters: 9,731,401 (27.2%)
Reads written (passing filters): 35,737,506 (100.0%)
Total basepairs processed: 1,286,550,216 bp
Total written (filtered): 1,271,732,933 bp (98.8%)
=== Adapter 1 ===
Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9731401 times
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1
Bases preceding removed adapters:
A: 23.5%
C: 0.4%
G: 34.6%
T: 41.5%
none/other: 0.0%
Overview of removed sequences
length count expect max.err error counts
1 5687303 8934376.5 0 5687303
2 3330707 2233594.1 0 3330707
3 493277 558398.5 0 493277
4 197883 139599.6 0 197883
5 6244 34899.9 0 6244
6 4928 8725.0 0 4928
7 2348 2181.2 0 2348
8 1598 545.3 0 1598
9 1419 136.3 0 1022 397
10 1364 34.1 1 753 611
11 1161 8.5 1 699 462
12 569 2.1 1 379 190
13 283 0.5 1 247 36
14 204 0.5 1 172 32
15 151 0.5 1 128 23
16 141 0.5 1 127 14
17 109 0.5 1 83 26
18 101 0.5 1 88 13
19 79 0.5 1 68 11
20 100 0.5 1 84 16
21 109 0.5 1 92 17
22 75 0.5 1 65 10
23 70 0.5 1 59 11
24 65 0.5 1 54 11
25 56 0.5 1 52 4
26 61 0.5 1 50 11
27 114 0.5 1 98 16
28 46 0.5 1 39 7
29 81 0.5 1 60 21
30 54 0.5 1 44 10
31 29 0.5 1 26 3
32 42 0.5 1 33 9
33 60 0.5 1 42 18
34 72 0.5 1 59 13
35 72 0.5 1 59 13
36 426 0.5 1 141 285
Successfully deleted temporary file pancreas_qual_trimmed.fastq
RUN STATISTICS FOR INPUT FILE: pancreas
=============================================
35737506 sequences processed in total
Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 0 (0.0%)
Sequences removed because they became shorter than the length cutoff of 20 bp: 2113 (0.0%)
RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 9730903 (27.2%)
>>> Now running FastQC on the data <<<
Started analysis of pancreas_trimmed.fq
Too many tiles (>1000) so giving up trying to do per-tile qualities since we're probably parsing the file wrongly
Approx 5% complete for pancreas_trimmed.fq
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Analysis complete for pancreas_trimmed.fq
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